Commit 85505a9d authored by bue's avatar bue 🐮

@ annotTutorial : smoketest evolution

parent b0e72616
{"1": {"endpoint": null, "iSpot": 1, "iWell": 1, "iixii": "1_1x1_1", "ixi": "1x1", "perturbation": null, "sample": {"MCF10A_CVCL0598": {"batch": "ICBP43", "catalogNu": "CRL-10317", "conc": 5000, "concUnit": "cells_per_mL_uo0000201", "cultType": "batch", "externalId": "LCL-2085", "manufacture": "ATCC_Own", "passageOrigin": 7, "passageUsed": 13, "recordSet": "cl-MCF10A-p7x13cpml5000h72", "timeBegin": 0, "timeEnd": 72, "timeUnit": "hour_uo0000032"}}, "sxi": "Ax1"}, "acid": "acpipe_acjson-cl-MCF10A-p7x13cpml5000h72_ac.json", "log": null, "runid": "cl-MCF10A-p7x13cpml5000h72", "runtype": "acpipe_acjson", "spotlayout": [1], "welllayout": "1x1"}
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{"1": {"endpoint": null, "iSpot": 1, "iWell": 1, "iixii": "1_1x1_1", "ixi": "1x1", "perturbation": null, "sample": {"MCF10A_CVCL0598": {"batch": "ICBP43", "catalogNu": "CRL-10317", "conc": 5000, "concUnit": "cells_per_mL_uo0000201", "cultType": "batch", "externalId": "LCL-2085", "manufacture": "ATCC_Own", "passageOrigin": 7, "passageUsed": 9, "recordSet": "cl-MCF10A-p7x9cpml5000h72", "timeBegin": 0, "timeEnd": 72, "timeUnit": "hour_uo0000032"}}, "sxi": "Ax1"}, "acid": "acpipe_acjson-cl-MCF10A-p7x9cpml5000h72_ac.json", "log": null, "runid": "cl-MCF10A-p7x9cpml5000h72", "runtype": "acpipe_acjson", "spotlayout": [1], "welllayout": "1x1"}
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......@@ -16,8 +16,7 @@ import json
# acpipe library
# check out: https://gitlab.com/biotransistor/acpipe_acjson
#import acpipe_acjson.acjson as ac
import acpipe_acjsonDev.acpipe_acjson.acjson as ac
import acpipe_acjson.acjson as ac
# load samplesetsets
with open('../../experiment_acjson/acaxis/acpipe_acjson-cl-HCC1954-p0x3cpml1250000h72_ac.json') as f_json:
......@@ -39,16 +38,16 @@ with open('../../experiment_acjson/superset/acpipe_aushon-es8C002_ac.json') as f
d_es8c002 = json.load(f_json)
# fuse acaxis acjson files
# acfuseobject (0011)
# acfuseobject (0011) cl and es and ss
d_memali8c00201 = ac.acfuseobject(
s_runid='mema-LI8C00201',
d_acjsonsample=d_clhcc1954p0x3cpml1250000h72,
d_acjsonperturbation=d_es8c002,
d_acjsonendpoint=d_ss100v1,
s_runtype='acpipe_acjson',
s_runtype='annot_runset',
)
# acfuserepeat0011
# acfuserepeat0011 ls and ds
ac.acfuserepeat0011(
d_acjsonmajor=d_memali8c00201,
d_acjsonminor=d_ls1layout1v3,
......
###
# title: acpipeTemplateCode_mema-LI8C00202.py
#
# date: 2018-03-30
# license: GPL>=3
# author: bue
#
# description:
# acpipe script to generate a runset related acjson file.
# template automatically generated by annot softawre.
# check out: https://gitlab.com/biotransistor/annot
###
# python library
import json
# acpipe library
# check out: https://gitlab.com/biotransistor/acpipe_acjson
import acpipe_acjson.acjson as ac
# load samplesetsets
with open('../../experiment_acjson/acaxis/acpipe_acjson-cl-HCC1954-p0x3cpml1250000h72_ac.json') as f_json:
d_clhcc1954p0x3cpml1250000h72 = json.load(f_json)
# load perturbationsetsets
with open('../../experiment_acjson/acaxis/acpipe_acjson-ds-Lapatinib1v1_ac.json') as f_json:
d_dslapatinib1v1 = json.load(f_json)
with open('../../experiment_acjson/acaxis/acpipe_acjson-ls-2layout1v3_ac.json') as f_json:
d_ls2layout1v3 = json.load(f_json)
# load endpointsetsets
with open('../../experiment_acjson/acaxis/acpipe_acjson-ss-100v1_ac.json') as f_json:
d_ss100v1 = json.load(f_json)
# load supersetset
with open('../../experiment_acjson/superset/acpipe_aushon-es8C002_ac.json') as f_json:
d_es8c002 = json.load(f_json)
# fuse acaxis acjson files
# acfuseobject (0011) cl and es and ss
d_memali8c00202 = ac.acfuseobject(
s_runid='mema-LI8C00202',
d_acjsonsample=d_clhcc1954p0x3cpml1250000h72,
d_acjsonperturbation=d_es8c002,
d_acjsonendpoint=d_ss100v1,
s_runtype='annot_runset',
)
# acfuserepeat0011 ls and ds
ac.acfuserepeat0011(
d_acjsonmajor=d_memali8c00202,
d_acjsonminor=d_ls2layout1v3,
s_ambiguous='break',
b_deepcopy=False,
)
ac.acfuserepeat0011(
d_acjsonmajor=d_memali8c00202,
d_acjsonminor=d_dslapatinib1v1,
s_ambiguous='break',
b_deepcopy=False,
)
# update log
d_memali8c00202["log"] = "{} + {} + {} + {} + {}".format(
d_clhcc1954p0x3cpml1250000h72['acid'],
d_es8c002['acid'],
d_ls2layout1v3['acid'],
d_dslapatinib1v1['acid'],
d_ss100v1['acid'],
)
# write to json file
with open(d_memali8c00202['acid'], 'w') as f_acjson:
json.dump(d_memali8c00202, f_acjson, sort_keys=True)
###
# title: acpipeTemplateCode_mema-LI8C00203.py
#
# date: 2018-03-31
# license: GPL>=3
# author: bue
#
# description:
# acpipe script to generate a runset related acjson file.
# template automatically generated by annot softawre.
# check out: https://gitlab.com/biotransistor/annot
###
# python library
import json
# acpipe library
# check out: https://gitlab.com/biotransistor/acpipe_acjson
import acpipe_acjson.acjson as ac
# load samplesetsets
with open('../../experiment_acjson/acaxis/acpipe_acjson-cl-HCC1954-p0x3cpml1250000h72_ac.json') as f_json:
d_clhcc1954p0x3cpml1250000h72 = json.load(f_json)
# load perturbationsetsets
with open('../../experiment_acjson/acaxis/acpipe_acjson-ds-Lapatinib1v1_ac.json') as f_json:
d_dslapatinib1v1 = json.load(f_json)
with open('../../experiment_acjson/acaxis/acpipe_acjson-ls-3layout1v3_ac.json') as f_json:
d_ls3layout1v3 = json.load(f_json)
# load endpointsetsets
with open('../../experiment_acjson/acaxis/acpipe_acjson-ss-100v1_ac.json') as f_json:
d_ss100v1 = json.load(f_json)
# load supersetset
with open('../../experiment_acjson/superset/acpipe_aushon-es8C002_ac.json') as f_json:
d_es8c002 = json.load(f_json)
# acfuseobject (0011)
d_memali8c00203 = ac.acfuseobject(
s_runid='mema-LI8C00203',
d_acjsonsample=d_clhcc1954p0x3cpml1250000h72,
d_acjsonperturbation=d_es8c002,
d_acjsonendpoint=d_ss100v1,
s_runtype='annot_runset',
)
# acfuserepeat0011
ac.acfuserepeat0011(
d_acjsonmajor=d_memali8c00203,
d_acjsonminor=d_ls3layout1v3,
s_ambiguous='break',
b_deepcopy=False,
)
ac.acfuserepeat0011(
d_acjsonmajor=d_memali8c00203,
d_acjsonminor=d_dslapatinib1v1,
s_ambiguous='break',
b_deepcopy=False,
)
# update log
d_memali8c00203['log'] = '{} + {} + {} + {} + {}'.format(
d_clhcc1954p0x3cpml1250000h72['acid'],
d_dslapatinib1v1['acid'],
d_ls3layout1v3['acid'],
d_ss100v1['acid'],
d_es8c002['acid'],
)
# write to json file
with open(d_memali8c00203['acid'], 'w') as f_acjson:
json.dump(d_memali8c00203, f_acjson, sort_keys=True)
###
# title: acpipeTemplateCode_mema-LI8C00204.py
#
# date: 2018-03-31
# license: GPL>=3
# author: bue
#
# description:
# acpipe script to generate a runset related acjson file.
# template automatically generated by annot softawre.
# check out: https://gitlab.com/biotransistor/annot
###
# python library
import json
# acpipe library
# check out: https://gitlab.com/biotransistor/acpipe_acjson
import acpipe_acjson.acjson as ac
# load samplesetsets
with open('../../experiment_acjson/acaxis/acpipe_acjson-cl-HCC1954-p0x3cpml1250000h72_ac.json') as f_json:
d_clhcc1954p0x3cpml1250000h72 = json.load(f_json)
# load perturbationsetsets
with open('../../experiment_acjson/acaxis/acpipe_acjson-ds-Lapatinib1v1_ac.json') as f_json:
d_dslapatinib1v1 = json.load(f_json)
with open('../../experiment_acjson/acaxis/acpipe_acjson-ls-4layout2v3_ac.json') as f_json:
d_ls4layout2v3 = json.load(f_json)
# load endpointsetsets
with open('../../experiment_acjson/acaxis/acpipe_acjson-ss-100v1_ac.json') as f_json:
d_ss100v1 = json.load(f_json)
# load supersetset
with open('../../experiment_acjson/superset/acpipe_aushon-es8C002_ac.json') as f_json:
d_es8c002 = json.load(f_json)
# fuse acaxis acjson files
# acfuseobject (0011) cl and es and ss
d_memali8c00204 = ac.acfuseobject(
s_runid='mema-LI8C00204',
d_acjsonsample=d_clhcc1954p0x3cpml1250000h72,
d_acjsonperturbation=d_es8c002,
d_acjsonendpoint=d_ss100v1,
s_runtype='annot_runset',
)
# acfuserepeat0011 ls
ac.acfuserepeat0011(
d_acjsonmajor=d_memali8c00204,
d_acjsonminor=d_ls4layout2v3,
s_ambiguous='break',
b_deepcopy=False,
)
# acfuserepeat0011 ds
ac.acfuserepeat0011(
d_acjsonmajor=d_memali8c00204,
d_acjsonminor=d_dslapatinib1v1,
s_ambiguous='break',
b_deepcopy=False,
)
# update log and relabel
s_log ='{} + {} + {} + {} + {}'.format(
d_clhcc1954p0x3cpml1250000h72['acid'],
d_dslapatinib1v1['acid'],
d_ls4layout2v3['acid'],
d_ss100v1['acid'],
d_es8c002['acid'],
)
ac.acrelabel(
s_runid='mema-LI8C00204',
s_log=s_log,
d_iacjson=d_memali8c00204,
s_runtype='annot_runset',
b_deepcopy=False
)
# write to json file
with open(d_memali8c00204['acid'], 'w') as f_acjson:
json.dump(d_memali8c00204, f_acjson, sort_keys=True)
###
# title: acpipeTemplateCode_cl-MCF10A-p7x13cpml5000h72.py
#
# date: 2018-03-30
# license: GPL>=3
# author: bue
#
# description:
# acpipe script to generate a sampleset related acjson file.
# template automatically generated by annot softawre.
# check out: https://gitlab.com/biotransistor/annot
###
# python library
import copy
import json
# acpipe library
# check out: https://gitlab.com/biotransistor/acpipe_acjson
import acpipe_acjson.acjson as ac
# build acjson
d_acjson = ac.acbuild(
s_welllayout='1x1',
s_runid='cl-MCF10A-p7x13cpml5000h72',
s_runtype='acpipe_acjson'
)
# reagent: human-MCF10A_CVCL0598-ATCCOwn_CRL10317_ICBP43
s_gent = 'MCF10A_CVCL0598'
d_record = {s_gent: copy.deepcopy(ac.d_RECORDLONG)}
d_record[s_gent].update(copy.deepcopy(ac.d_SAMPLE))
d_record[s_gent].update(copy.deepcopy(ac.d_SET))
d_record[s_gent].update(copy.deepcopy(ac.d_EXTERNALID))
d_record[s_gent].update({'passageOrigin': 7})
d_record[s_gent].update({'passageUsed': 13})
d_record[s_gent].update({'manufacture': 'ATCC_Own'})
d_record[s_gent].update({'catalogNu': 'CRL-10317'})
d_record[s_gent].update({'batch': 'ICBP43'})
d_record[s_gent].update({'conc': 5000})
d_record[s_gent].update({'concUnit': 'cells_per_mL_uo0000201'})
d_record[s_gent].update({'cultType': 'batch'})
d_record[s_gent].update({'timeBegin': 0})
d_record[s_gent].update({'timeEnd': 72})
d_record[s_gent].update({'timeUnit': 'hour_uo0000032'})
d_record[s_gent].update({'recordSet': 'cl-MCF10A-p7x13cpml5000h72'})
d_record[s_gent].update({'externalId': 'LCL-2085'})
d_acjson = ac.acfuseaxisrecord(
d_acjson,
s_coor='1',
s_axis='sample',
d_record=d_record
)
# write to json file
print('write file: {}'.format(d_acjson['acid']))
with open(d_acjson['acid'], 'w') as f_acjson:
json.dump(d_acjson, f_acjson, sort_keys=True)
###
# title: acpipeTemplateCode_cl-MCF10A-p7x9cpml5000h72.py
#
# date: 2018-03-30
# license: GPL>=3
# author: bue
#
# description:
# acpipe script to generate a sampleset related acjson file.
# template automatically generated by annot softawre.
# check out: https://gitlab.com/biotransistor/annot
###
# python library
import copy
import json
# acpipe library
# check out: https://gitlab.com/biotransistor/acpipe_acjson
import acpipe_acjson.acjson as ac
# build acjson
d_acjson = ac.acbuild(
s_welllayout='1x1',
s_runid='cl-MCF10A-p7x9cpml5000h72',
s_runtype='acpipe_acjson'
)
# reagent: human-MCF10A_CVCL0598-ATCCOwn_CRL10317_ICBP43
s_gent = 'MCF10A_CVCL0598'
d_record = {s_gent: copy.deepcopy(ac.d_RECORDLONG)}
d_record[s_gent].update(copy.deepcopy(ac.d_SAMPLE))
d_record[s_gent].update(copy.deepcopy(ac.d_SET))
d_record[s_gent].update(copy.deepcopy(ac.d_EXTERNALID))
d_record[s_gent].update({'passageOrigin': 7})
d_record[s_gent].update({'passageUsed': 9})
d_record[s_gent].update({'manufacture': 'ATCC_Own'})
d_record[s_gent].update({'catalogNu': 'CRL-10317'})
d_record[s_gent].update({'batch': 'ICBP43'})
d_record[s_gent].update({'conc': 5000})
d_record[s_gent].update({'concUnit': 'cells_per_mL_uo0000201'})
d_record[s_gent].update({'cultType': 'batch'})
d_record[s_gent].update({'timeBegin': 0})
d_record[s_gent].update({'timeEnd': 72})
d_record[s_gent].update({'timeUnit': 'hour_uo0000032'})
d_record[s_gent].update({'recordSet': 'cl-MCF10A-p7x9cpml5000h72'})
d_record[s_gent].update({'externalId': 'LCL-2085'})
d_acjson = ac.acfuseaxisrecord(
d_acjson,
s_coor='1',
s_axis='sample',
d_record=d_record
)
# write to json file
print('write file: {}'.format(d_acjson['acid']))
with open(d_acjson['acid'], 'w') as f_acjson:
json.dump(d_acjson, f_acjson, sort_keys=True)
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